4CYY
The structure of vanin-1: defining the link between metabolic disease, oxidative stress and inflammation
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4CYF | PDB ENTRY 4CYF |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6 | THE PROTEIN WAS AT 15 MG/ML. THE RESERVOIR CONDITIONS WERE 25% (W/V) PEG 1500 PLUS 10% (V/V) SUCCINATE-PHOSPHATE-GLYCINE BUFFER AT PH 6.0. THE PLATES WERE SET UP AT 8 C AND THE DROPS WERE 150 NL PLUS 150 NL IN SITTING DROP PLATES. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.91 | 68.6 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 101.904 | α = 90 |
b = 101.904 | β = 90 |
c = 133.652 | γ = 120 |
Symmetry | |
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Space Group | P 32 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC CCD | 2013-11-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX2 | Australian Synchrotron | MX2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||||||
1 | 2.89 | 47.6 | 99.7 | 0.21 | 14.5 | 16.3 | 18526 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.89 | 3.04 | 97.9 | 1.12 | 2.7 | 16.1 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 4CYF | 2.89 | 88.25 | 17545 | 947 | 99.62 | 0.17646 | 0.17425 | 0.21883 | RANDOM | 61.539 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
2.84 | 1.42 | 2.84 | -9.23 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.198 |
r_dihedral_angle_4_deg | 18.372 |
r_dihedral_angle_3_deg | 15.288 |
r_dihedral_angle_1_deg | 7.031 |
r_mcangle_it | 4.309 |
r_scbond_it | 3.816 |
r_mcbond_it | 2.677 |
r_mcbond_other | 2.675 |
r_angle_refined_deg | 1.322 |
r_angle_other_deg | 0.71 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3615 |
Nucleic Acid Atoms | |
Solvent Atoms | 11 |
Heterogen Atoms | 84 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |
PHASER | phasing |